Yes it will work ..
Just at the time of mdrun add -cpi cpt ( prvious cpt file )
With best wishes and regards..!!
On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
for my original MD, based on mdp file the total time is 500 ps. After it
finished, I have
Dear All,
for my original MD, based on mdp file the total time is 500 ps. After it
finished, I have decided to extend the MD run to 2.5 ns.
I think the following command should be used:
tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr
But as for in the original mdp file
Hello,
I have a system with a glucose molecule.
I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.
[ O8 ]
8 18
10 is oxygen no. and 20 is hydroen no.
But, if I try to use g_dipoles to get the dipole
Nilesh Dhumal wrote:
Hello,
I have a system with a glucose molecule.
I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.
[ O8 ]
8 18
10 is oxygen no. and 20 is hydroen no.
I'm assuming you mean 8 is
Dear Gromacs users,
I am running a CG simulation for a peptide in lipid bilayer, and the
run didnot extend after 42000 ps using gromacs 4.0.7,
Reading toplogy and shit from memb12extnr42000ns.tpr
Extending remaining runtime of by 1e+06 ps (now -2144967266 steps)
You've simulated long enough. Not
ram bio wrote:
Dear Gromacs users,
I am running a CG simulation for a peptide in lipid bilayer, and the
run didnot extend after 42000 ps using gromacs 4.0.7,
Reading toplogy and shit from memb12extnr42000ns.tpr
Extending remaining runtime of by 1e+06 ps (now -2144967266 steps)
You've
Hi Justin,
The command was:
tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr
Thanks
Ram
On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote:
ram bio wrote:
Dear Gromacs users,
I am running a CG simulation for a peptide in lipid bilayer,
ram bio wrote:
Hi Justin,
The command was:
tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr
Try using -nsteps instead. There are issues with -extend and -until (bad
rounding, limits to the size of the number, etc) that can cause this problem. I
believe all
?
Berk
Date: Mon, 13 Dec 2010 11:40:50 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Re: tpbconv extension
ram bio wrote:
Hi Justin,
The command was:
tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr
Try using
Hi,
I fixed the bug for 4.5.4.
If you want an unlimited number of steps, use:
tpbconv -nsteps -1
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Re: tpbconv extension
Date: Mon, 13 Dec 2010 17:44:53 +0100
Hi,
No this is actually a bug in tpbconv
Hi Justin and Berk,
Thanks for the suggestions.
I am using gromacs 4.0.7 single precision, and would like to extend my
run each time by 1 microsec as it fits into the wall time on the
server for my system.
Please suggest.
Thanks
Ram
On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul
reasons), you might want to consider
upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before).
Berk
Date: Mon, 13 Dec 2010 17:56:43 +0100
Subject: Re: [gmx-users] Re: tpbconv extension
From: rmbio...@gmail.com
To: jalem...@vt.edu; gmx-users@gromacs.org
CC:
Hi Justin and Berk
(and possibly applying the bug-fix I mailed before).
Berk
Date: Mon, 13 Dec 2010 17:56:43 +0100
Subject: Re: [gmx-users] Re: tpbconv extension
From: rmbio...@gmail.com
To: jalem...@vt.edu; gmx-users@gromacs.org
CC:
Hi Justin and Berk,
Thanks for the suggestions.
I am using gromacs 4.0.7 single
many core and 4.5.3 will also improve your performance.
Berk
Date: Mon, 13 Dec 2010 18:16:28 +0100
Subject: Re: [gmx-users] Re: tpbconv extension
From: rmbio...@gmail.com
To: gmx-users@gromacs.org
Hi Berk,
Thanks for the suggestion, does the tpr file generated by the options
mention on PC
Dear David:
Thanks a lot for your reply. You are absolutely right! All the charges
in the tpr file is zero now.
This does not make much sense to me though, as the group I selected
with tpbconv does not include all the atoms. I also tried to use
other groups such as POPC or Protein and
Hi
I have always used tpbconv to do my restarts however after reading the newer
documentation, I have noticed that it only mentions that the energy file can be
used with Pressure Coupling or Noose Hoover temperature coupling, so what is
the correct usage when using berendsen temperature
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